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You should use a whitelist and only allow good search engines access to these sitemap files like Google and Bing.
This is a huge problem that I'm afraid most people don't even consider when submitting sitemap files to Google and Bing. I track every request to my xml sitemap files and I've denied access to over 6,500 IPs since I started doing this (3 months ...

The way you have created your new sitemap is correct. Each URL is listed only once inside <loc> tags but next to those are all the alternative URLs for the same page in other languages so it might seem that you are listing everything three times.
A sitemap index is used when you outgrow a single sitemap file. Sitemap files have a limit of 50,000 ...

I do not know if it is right to answer my own question. But after some days I finally found the solution.
I want to thank Alexey Ten for mentioning the word "module". It seems the pagespeed module is the problem. Disabling pagespeed in the nginx configuration files solved the problem. I've read pagespeed only changes html so probably pagespeed thought this ...